X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlinecommand.cpp;h=f1ec55cab12261a5b91f425553bf34bc71393727;hb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e;hp=09b16541930d34f795bba4ca182ed74b9054d8fc;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index 09b1654..f1ec55c 100644
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -9,20 +9,41 @@
 
 #include "getlinecommand.h"
 
-
-GetlineCommand::GetlineCommand(){
+//**********************************************************************************************************************
+GetlineCommand::GetlineCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			if (option != "") { mothurOut("There are no valid parameters for the get.line command."); mothurOutEndLine(); abort = true; }
+			
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the get.line command."); mothurOutEndLine(); abort = true; }				
+		}
+
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "GetlineCommand", "GetlineCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetlineCommand class function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void GetlineCommand::help(){
+	try {
+		mothurOut("The get.line command can only be executed after a successful read.otu command.\n");
+		mothurOut("You may not use any parameters with the get.line command.\n");
+		mothurOut("The get.line command should be in the following format: \n");
+		mothurOut("get.line()\n");
+		mothurOut("Example get.line().\n");
+	}
+	catch(exception& e) {
+		errorOut(e, "GetlineCommand", "help");
 		exit(1);
-	}	
-			
+	}
 }
 
 //**********************************************************************************************************************
@@ -34,37 +55,35 @@ GetlineCommand::~GetlineCommand(){
 
 int GetlineCommand::execute(){
 	try {
-		filename = globaldata->inputFileName;
+	
+		if (abort == true) { return 0; }
+	
 		ifstream in;
-		openInputFile(filename, in);
+		openInputFile(globaldata->inputFileName, in);
 		string label;
 		int numBins = 0;
 		int count = -1;
 		int line = 1;
-		while(in.good())
-		{
+		while(in.good()) {
 			if(count > numBins)
 				count = 0;
-			if(count == 0)
-			{
-				cout << line << "\n";
+			if(count == 0) {
+				mothurOut(toString(line)); mothurOutEndLine();
 				in >> numBins;
 				line++;
 			}
 			in >> label;
 			count++;
 		}
+		
+		in.close();
 		return 0;		
 	}
 
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "GetlineCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetlineCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }